The most common and most likely answer to this crossword clue is the 6 letter word TRITON
I've seen this crossword clue in The Guardian
T
R
I
T
O
N
Buddy explains!
The straight part
We know that "Main messenger coming to a fishy end" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case main messenger coming to a fishy end = triton.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does TRITON mean?
TRITON noun- The atomic nucleus of a tritium atom, consisting of a proton and two neutrons
- Any of several marine gastropods of the family Ranellidae, which have a pointed spiral shell.